Methods and compositions for synthetic biomarkers

Abstract

The present disclosure encompasses embodiments of nucleic acids comprising genetic elements which are useful for the detection of diseased cells.

1 .- 8 . (canceled) 
     
     
         9 . A method, comprising:
 (a) administering to a subject suspected of having a cancer a plurality of nanoplasmids, wherein said plurality of nanoplasmids comprises a plurality of different promoters of genes overexpressed in a tumor cell versus a normal tissue or functional fragments thereof operably linked to genes encoding reporter proteins, wherein said plurality of different promoters of genes overexpressed in said tumor cell versus said normal tissue drive expression of said reporter proteins in a cell affected by said cancer,   wherein a nanoplasmid of said plurality of nanoplasmids comprises: (i) a minimized bacterial Co1E1 or R6K origin of replication; and (ii) a bacterial RNA-based selectable marker; and   (b) localizing a tumor or an absence thereof in a body of said subject via expression of said reporter proteins using an imaging technique performed on said body of said subject.   
     
     
         10 .- 12 . (canceled) 
     
     
         13 . The method of  claim 9 , wherein said imaging technique further comprises photoacoustic imaging, Magnetic resonance imaging (MRI) imaging, positron emission tomography (PET) imaging, or single-photon emission computed tomography (SPECT) imaging. 
     
     
         14 . The method of  claim 9 , wherein said localizing said tumor or absence thereof comprises localizing said tumor. 
     
     
         15 . The method of  claim 14 , wherein said localizing said tumor has a minimum detectable tumor size of 3 mm 3 . 
     
     
         16 . The method of  claim 9 , wherein said localizing said tumor or said absence thereof is further performed at least 8 hours, at least 12 hours, at least 24 hours, at least 36 hours, at least 48 hours, at least 72 hours following said introducing in (a). 
     
     
         17 . The method of  claim 9 , wherein said subject further has at least one symptom of cancer. 
     
     
         18 . The method of  claim 17 , wherein said at least one symptom further comprises a positive signal on a mammogram or from a cancer screening diagnostic test, disproportionate blood cell distribution, weight loss, swollen lumps or glands, night sweats, blood in urine, blood in stool, unexpected bleeding or discharge from body including nipples, dizziness, blurred vision or loss of balance, diarrhea, acute pain, low grade fever, constipation, loss of appetite, nagging cough or hoarseness, or jaundice. 
     
     
         19 . The method of  claim 9 , wherein said subject has at least one risk factor for cancer such as, Li-Fraumeni syndrome, lynch syndrome, familial adenomatous polyposis, lung nodules, Von Hippel-Lindau disease, aplastic anemia, myelodysplastic syndrome, Cowden syndrome, hereditary breast and ovarian cancer syndrome (HBOC), or BRCA mutations; being a current smoker, ex-smoker, or exposed to heavy doses of second hand smoke; exposure to carcinogens, excessive sunlight, immunosuppressive agents, or hepatitis B, hepatitis C, or human papilloma virus; or obesity. 
     
     
         20 . The method of  claim 9 , wherein said subject has previously received surgical, chemotherapeutic, radiological or immunotherapeutic treatment for cancer. 
     
     
         21 . The method of  claim 9 , wherein said reporter proteins further comprise enzyme reporters or peptide epitope tags. 
     
     
         22 . The method of  claim 21 , wherein the reporter proteins comprise said peptide epitope tags, and wherein said imaging technique further comprises administration of a labeled peptide binding element that recognizes said peptide epitope tags. 
     
     
         23 . The method of  claim 9 , wherein said plurality of different promoters of genes overexpressed in said tumor cell versus said normal tissue or functional fragments thereof further comprise AGR2, CST1, FAM1 11B, CEP55, CEACAM5, or KIF20A. 
     
     
         24 . The method of  claim 9 , wherein said nanoplasmids further comprise: (i) a minimized bacterial ColE1 or R6K origin of replication; and (ii) a bacterial RNA-selectable marker. 
     
     
         25 . The method of  claim 9 , wherein said plurality of nanoplasmids is administered subcutaneously, intraventricularly, intrathecally, intracerebroventricularly, transdermally, intramuscularly, orally by inhalation, nasally, rectally, intratumorally, proxi-tumorally, or into a lymph node in said subject. 
     
     
         26 . The method of  claim 9 , wherein said reporter protein encodes a therapeutically effective agent. 
     
     
         27 . The method of  claim 9 , wherein said tumor cell is not a virally-infected cell. 
     
     
         28 . The method of  claim 9 , wherein said nanoplasmids are provided as part of a composition comprising a transfection agent. 
     
     
         29 . The method of  claim 28 , wherein said transfection agent comprises lipophilic nanoparticles. 
     
     
         30 . The method of  claim 28 , wherein said transfection agent comprises a polyethylenimine. 
     
     
         31 . The method of  claim 28 , wherein said transfection agent comprises a poly(β-amino ester).